[BioC] Help with HyperGTest

James W. MacDonald jmacdon at med.umich.edu
Tue Nov 10 18:38:31 CET 2009


Hi Yue,

Yue, Chen - BMD wrote:
> Dear All,
> 
> I hope to get some help on the hyperGTest in GOstats. I want to do an GO enrichment anlaysis on a set of E. coli K12 genes (substr DH10B). I attached the target id file, partial ecoli id file (as universeGeneIds) and sessionInfo to the email. The following is my commands and error. It seems that my gene id is not found in the annotation package but I don't know how to find out what gene ids are included in the package. I used "org.EcK12.eg.db" package which uses Entrez ids and my R version is 2.9.2 on WinXP. Should I use a different annotation package? Thank you very much!
> 
>> targettable <- read.table("D:/RProjects/targetids.txt")
>> ecolitable <- read.table("D:/RProjects/ecoliids.txt")
>> targetids <- unique(targettable[,1])
>> ecoliids <- unique(ecolitable[,1])
>> params = new("GOHyperGParams", geneIds=targetids, universeGeneIds=ecoliids, annotation="org.EcK12.eg.db", ontology="BP", pvalueCutoff=0.01, conditional=FALSE, testDirection="over")
>> BPoverTest = hyperGTest(params)
> Error in getUniverseHelper(probes, datPkg, entrezIds) : 
>   After filtering, there are no valid IDs that can be used as the Gene universe.
>   Check input values to confirm they are the same type as the central ID used by your annotation package.
>   For chip packages, this will still mean the central GENE identifier used by the package (NOT the probe IDs).

Your error message indicates that the ecoliids are not Entrez Gene IDs. 
Your attachments were stripped so we can't look at these data, but you 
can give us an idea by using e.g., head(ecoliids) and supplying us with 
the output.

Best,

Jim


> 
> Regards,
> 
> Yue
> 
> 
> 
> This email is intended only for the use of the individual or entity to which it is addressed and may contain information that is privileged and confidential. If the reader of this email message is not the intended recipient, you are hereby notified that any dissemination, distribution, or copying of this communication is prohibited. If you have received this email in error, please notify the sender and destroy/delete all copies of the transmittal. Thank you.
> 
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826



More information about the Bioconductor mailing list